Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells
EDPIECEPOINT(1) EDPIECEPOINT(1)
NAME
edpiecepoint - edit a list of piece coordinates
SYNOPSIS
edpiecepoint
DESCRIPTION
This program allows one to "edit" a list of piece coordinates, or a list of
integer point coordinates, in three ways:
1) The set of Z values may be mapped, one-to-one, to any arbitrary new set
of Z values; and
2) The X, Y or Z coordinates of all pieces or points may be shifted by a
constant.
3) The overlap between pieces can be changed.
In addition, one can create a new piece list for single frame images or
montaged images. The pieces can be ordered in rows or in columns.
The remapping of Z values is specified by a list of values (comma-separated
ranges, e.g. 0-3,5-7). This list must have the same number of Z values as
in the input list of Z values. The Z values in the input list will be
mapped one-to-one onto the new list. Enter "/" to take the input list
without modification Enter numbers between -999 and -990 to delete points
with a particular Z value; e.g. if the input list has Z values from 0 to 9,
entering 0-4,-999,5-8 will delete all points with Z between 4.5 and 5.5, and
shift the Z of points with Z greater then 5.5 down by 1. If the input list
has Z from 0-19, entering 0-9,-999--990 will remove all pooints with Z from
10 to 19. Enter -1 to replace each Z value with its negative.
When you create a new piece list, you control the overlap between pieces by
entering a spacing instead. This spacing is the frame size minus the
overlap; e.g., for a size of 2048 and an overlap of 10%, one would enter
2048 - 204 = 1844. Spacing can be measured by taking the difference between
the coordinates of corresponding points in adjacent pieces. For example, if
a feature is at an X coordinate of 1800 in one piece and at 100 in the piece
to the right, then the spacing in X is 1800 - 100 = 1700. Enter a negative
number for X spacing if pieces are ordered from right to left, or a negative
number for Y spacing if pieces are ordered from top to bottom. Enter / if
you just have one piece.
Edpiecepoint uses the PIP package for input (see the manual page for pip)
and can still take sequential input interactively. The following options
can be specified either as command line arguments (with the -) or one per
line in a command file or parameter file (without the -):
-input OR -InputFile File name
Input piece list or point file. If this option is not entered and -create
is not entered, the first non-optional argument will be used for an input
file.
-output OR -OutputFile File name
Output piece list or point file. If this option is not entered, the
second non-optional argument will be used if -create is not entered;
otherwise the first non-option argument will be used for an output file.
-create OR -CreateForSections Integer
Number of sections to create a new piece list for
-pieces OR -PiecesInXandY Two integers
Number of pieces in X and Y in the newly created piece list
-spacing OR -SpacingInXandY Two integers
Spacing between the pieces in X and Y in the newly created piece list.
Enter the negative of a spacing to have pieces coordinates put out in
inverse order, from high to low coordinates. For how to determine the
desired spacing, see above.
-columns OR -ColumnsOfPieces
Order pieces in a newly created piece list so that successive pieces occur
in columns (in Y) rather than in rows (in X).
-divide OR -DivideByBinning Integer
This option can be used to make a new piece list that works with binned
images. Rather than just dividing the existing coordinates by the
binning, the program determines a new overlap value and makes sure that
coordinates are regularly spaced apart. To do this, it needs the image
sizes before and after binning, entered with -size and -binned.
-overlap OR -NewOverlapInXandY Two integers
This option can be used to change the overlap between pieces in a piece
list. Enter the new overlaps in X and Y, and enter the size of the pieces
with the -size option.
-size OR -SizeInXandY Two integers
Size of pieces in X and Y. This entry is required to adjust overlap or to
divide by binning; in the latter case enter the full size of the unbinned
images to which the input piece list corresponds.
-binned OR -BinnedSizeInXandY Two integers
New, binned size of pieces in X and Y (required to divide by binning)
-new OR -NewZList List of integer ranges
List of Z values to map old list to. There must be as many values in this
list as in the list of Z values to remap. See notes above on the contents
of this list.
-add OR -AddToAllCoordinates Three floats
Amount to add to all coordinates in X, Y, and Z, after remapping
-param OR -ParameterFile Parameter file
Read parameter entries as keyword-value pairs from a parameter file.
-help OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
If there are no command-line arguments, Edpiecepoint takes sequential input
the old way, with the following entries:
Name of input piece or point list file, or Return if none
IF you enter "Return", then the program will create a new piece
list. Then make the following 4 entries:
Number of sections (N) for which to make piece coordinates. The Z
coordinates will initially run from 0 to N-1, and the lower left X and
Y coordinates will be 0.
Number of pieces in X and in Y (enter / for 1,1)
Spacing between pieces in X and in Y. See above.
0 if pieces progress along rows in the image file, or 1 if they progress
along columns.
Name of output piece or point list file
New list of Z values. See above.
Amounts to add to all X, Y, and Z coordinates. These values will be
added after the remapping of Z values, if any.
HISTORY
Written by David Mastronarde, 5/8/89